Seniors who got flu shots received minimal protection against the most pervasive flu strain of the season—one of the worst in recent years — according to a government report released Thursday.

For people 65 and older, the vaccination was just 9% effective, less than one-fifth as effective as for the general population, according to the Centers for Disease Control and Prevention. Across all age groups, the flu shot was moderately effective at 56%, a rate similar to previous years, the CDC said. The effectiveness rate means seniors who got the shot were just 9% less likely to get the flu than those who went without.

It isn’t clear why the flu shot provided such little resistance for seniors against the season’s dominant circulating strain, the H3N2 virus. For all three strains the vaccination protects against, including the less-prevalent Influenza B virus, the flu shots had an effectiveness rate of 27%, the CDC said.“We’re well aware that influenza vaccines, in particular, work less effectively as you get older,” said Joseph Bresee, a medical epidemiologist at the CDC.

Researchers can’t fully explain why flu shots are less effective with seniors, beyond the fact that older people have weaker immune systems. In recent years, a more powerful dosage of the flu shot was launched with older patients in mind, though it isn’t widely available. Also, vaccines could be augmented with additives that could boost immune systems. Neither approach has been thoroughly evaluated.

The CDC study, which tracked nearly 2,700 children and adults who developed flulike illnesses in December and January, is a preliminary estimate of the seasonal flu shot’s efficacy. The data for seniors is limited to about 300 people.

Due to the mildness of the last flu season, the CDC wasn’t able to track how effective vaccinations were with people 65 and older. But for the 2010-11 season, the flu shot was found to be about 36% effective for seniors, the CDC said.

The data underscore the need for a better vaccine for the elderly and add to the debate over whether the same flu shot should be administered to everyone. People 65 and older are among the most at-risk demographics for contracting the flu, due to their weaker immune systems. Within the next several years, Mr. Bresee believes a targeted or tailored flu vaccine could become broadly available.

CDC officials had cautioned that this flu season, which arrived a month earlier than usual, could be the most severe since 2003-04, when about 48,600 people died from influenza, or about double the historic average of around 24,000.

The flu season peaked at the end of last year and the first week of January, when 47 states reported high levels of influenza-like illness, according to the CDC.